<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jul 14, 2009, at 2:07 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="font-family: monospace; ">If you mean "residues that are in the amber parm file and thus don't <br>require running antechamber" I don't know of a command-line specifier <br>for exactly that, although the above may work in many cases.</span></span></blockquote><div><br></div>If you do "addcharge standard" which adds charges to the residues that Amber has in its parameter files, then "sel :/amberName" will select those residues only. The addcharge command (and Add Charge tool) adds the amberName residue attribute as the name used by Amber for that residue (e.g. CYN for N-terminal cysteine).</div><div><br></div><div>--Eric</div><div><br><br></div><div><br></div><br></body></html>